+Open data
-Basic information
Entry | Database: PDB / ID: 5vaq | ||||||
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Title | Crystal Structure of Beta-Klotho in Complex with FGF21CT | ||||||
Components |
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Keywords | SIGNALING PROTEIN / (beta/alpha) 8 Receptor for Endocrine FGF | ||||||
Function / homology | Function and homology information positive regulation of triglyceride catabolic process / Cellular hexose transport / response to methionine / positive regulation of low-density lipoprotein receptor activity / betaKlotho-mediated ligand binding / Assembly of active LPL and LIPC lipase complexes / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of low-density lipoprotein particle clearance / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 ...positive regulation of triglyceride catabolic process / Cellular hexose transport / response to methionine / positive regulation of low-density lipoprotein receptor activity / betaKlotho-mediated ligand binding / Assembly of active LPL and LIPC lipase complexes / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of low-density lipoprotein particle clearance / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 / endothelial cell apoptotic process / cellular response to low-density lipoprotein particle stimulus / cellular response to glucagon stimulus / fibroblast growth factor binding / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / negative regulation of endothelial cell apoptotic process / SHC-mediated cascade:FGFR4 / hydrolase activity, hydrolyzing O-glycosyl compounds / endoplasmic reticulum unfolded protein response / FRS-mediated FGFR4 signaling / regulation of cell migration / response to nutrient levels / response to activity / positive regulation of glucose import / cellular response to glucose stimulus / animal organ morphogenesis / Negative regulation of FGFR4 signaling / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to xenobiotic stimulus / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cold-induced thermogenesis / RAF/MAP kinase cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cell differentiation / carbohydrate metabolic process / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å | ||||||
Authors | Lee, S. / Schlessinger, J. | ||||||
Citation | Journal: Nature / Year: 2018 Title: Structures of beta-klotho reveal a 'zip code'-like mechanism for endocrine FGF signalling. Authors: Lee, S. / Choi, J. / Mohanty, J. / Sousa, L.P. / Tome, F. / Pardon, E. / Steyaert, J. / Lemmon, M.A. / Lax, I. / Schlessinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vaq.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vaq.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vaq_validation.pdf.gz | 468.3 KB | Display | wwPDB validaton report |
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Full document | 5vaq_full_validation.pdf.gz | 476.8 KB | Display | |
Data in XML | 5vaq_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 5vaq_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/5vaq ftp://data.pdbj.org/pub/pdb/validation_reports/va/5vaq | HTTPS FTP |
-Related structure data
Related structure data | 5vakC 5vanC 5v9q 5v9r C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 109594.398 Da / Num. of mol.: 1 / Fragment: UNP residues30-983 / Mutation: N308Q, N611Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLB / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q86Z14 |
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#2: Antibody | Mass: 14837.451 Da / Num. of mol.: 1 / Fragment: Nanobody Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 |
#3: Antibody | Mass: 2397.512 Da / Num. of mol.: 1 / Fragment: UNP residues 186-209 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NSA1 |
#4: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.77 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6 / Details: 14% PEG 4000, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.606→64.007 Å / Num. obs: 46776 / % possible obs: 98 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09048 / Net I/σ(I): 13.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.606→64.007 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.46 Å2 / Biso mean: 63.4244 Å2 / Biso min: 37.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.606→64.007 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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